Biology subjects

Peterson, D. A.

Publications and source records attributed to Peterson, D. A..

4 recordsLinked to original sources

bioRxiv2025

Aged brain multi-omic integration captures immunometabolic and sex variation

Resolving the molecular basis for heterogeneous ageing in the human brain requires integrating its diverse molecular layers. Here we applied a tensor-decomposition framework to jointly analyse single-nucleus RNA-seq, DNA methylation, H3K9ac histone acetylation and proteomic data from 276 post-mortem human cortices. The analysis uncovered two dominant, multi-omic themes. First, we identified an immunometabolic axis characterised by microglial activation, suppression of PI3K-Akt-mTOR signalling and epigenetic signatures that suggest repurposing of developmental transcription factors such as BARHL1. Second, we decomposed the effect of sex into a multi-omic program linked to cellular plasticity: although driven by canonical sex-chromosome genes, this axis was epigenetically enriched for pathways regulating stem-cell pluripotency and exhibited a female-biased shift toward precursor-like states in the oligodendrocyte lineage. Together, these findings deliver a high-resolution atlas of glial ageing and demonstrate that broad risk factors manifest as complex, cell-specific vulnerabilities; an insight critical for the development of targeted therapeutic strategies.

neuroscience↗

bioRxiv2024

Mitochondrial Dysfunction in Alzheimer's Disease Is Driven By Excess ER-Calcium Release in Patient-Derived Neurons

Tight regulation of mitochondrial Ca2+ is essential for neuronal bioenergetics and cellular metabolism. Ca2+ transfer from ER-localized ryanodine receptors (RyR) and inositol triphosphate receptors (IP3R) to the mitochondria maintains a steady Ca2+ source that fuels oxidative phosphorylation and ATP production. In Alzheimers disease (AD), RyR-evoked Ca2+ release is markedly increased, contributing to synaptic deficits, protein mishandling, and memory impairment. Here, we demonstrate that dysregulated RyR-Ca2+ release directly compromises mitochondrial activity and is an early contributor to AD cellular pathology. We measured an array of mitochondrial functions using fluorescent biosensors and optical imaging in RyR2-expressing HEK cells and iPSC-derived neurons from familial AD and nonAD patients. In neurons from AD patients, resting mitochondrial Ca2+ levels were elevated alongside increased free radical production and higher caspase-3 activity relative to nonAD neurons. RyR-evoked Ca2+ release further potentiated pathogenic mitochondrial responses in AD neurons, with increased Ca2+ uptake and exaggerated membrane depolarization. Additionally, clearance of damaged mitochondria was impaired in AD neurons, demonstrating consequences from dysfunctional lysosomes. Notably, impairments to mitochondria in AD neurons were largely prevented with the RyR negative allosteric modulator, Ryanodex. These findings highlight how excess RyR-Ca2+ release broadly contributes to early cellular pathology in AD which includes a cascade of ER, lysosomal, and mitochondrial deficits culminating in neuronal decline and degeneration. Additionally, pharmacological suppression of RyR-Ca2+ release preserves mitochondrial, ER and lysosomal function, thus providing a novel and effective therapeutic. Significance StatementMitochondrial dysfunction plays a central role in the cellular pathogenesis of Alzheimers disease, yet the upstream mechanisms driving these deficits remain largely unknown. Here, in human neurons derived from Alzheimers patients, we reveal how early Ca2+ mishandling through the ER-localized ryanodine receptor (RyR) is sensed by the mitochondria and triggers a pathogenic metabolic cascade. Pharmacologically restoring Ca2+ homeostasis reversed these deficits, including the increased free radicals and defective mitophagy, and restored the nonAD phenotype. The findings reveal the early neuronal signaling mechanisms that affect ER Ca2+ handling, proteolysis, and mitochondrial activity, highlighting the potential role of the dysregulated RyR as a therapeutic target for AD using clinically relevant model systems.

neuroscience↗

bioRxiv2022

Protein mishandling and impaired lysosomal proteolysis generated through calcium dysregulation in Alzheimer's disease

Impairments in neural lysosomal- and autophagic-mediated degradation of cellular debris contribute to neuritic dystrophy and synaptic loss. While these are well-characterized features of neurodegenerative disorders such as Alzheimers disease (AD), the upstream cellular processes driving deficits in pathogenic protein mishandling are less understood. Using a series of fluorescent biosensors and optical imaging in model cells, AD mouse models and human neurons derived from AD patients, we reveal a novel cellular signaling cascade underlying protein mishandling mediated by intracellular calcium dysregulation, an early component of AD pathogenesis. Increased Ca2+ release via the endoplasmic reticulum (ER) resident ryanodine receptor (RyR) is associated with reduced expression of the lysosome proton pump vATPase subunits (V1B2 and V0a1), resulting in lysosome deacidification and disrupted proteolytic activity in AD mouse models and human induced neurons (HiN). As a result of impaired lysosome digestive capacity, mature autophagosomes with hyperphosphorylated tau accumulated in AD murine neurons and AD HiN, exacerbating proteinopathy. Normalizing AD-associated aberrant RyR-Ca2+ signaling with the negative allosteric modulator, dantrolene (Ryanodex), restored vATPase levels, lysosomal acidification and proteolytic activity, and autophagic clearance of intracellular protein aggregates in AD neurons. These results highlight that prior to overt AD histopathology or cognitive deficits, aberrant upstream Ca2+ signaling disrupts lysosomal acidification and contributes to pathological accumulation of intracellular protein aggregates. Importantly, this is demonstrated in animal models of AD, and in human iPSC-derived neurons from AD patients. Furthermore, pharmacological suppression of RyR-Ca2+ release rescued proteolytic function, revealing a target for therapeutic intervention that has demonstrated effects in clinically-relevant assays. Significance StatementWe demonstrate in model cells, murine neuronal cultures, and iPSC-derived human neurons, that AD associated RyR-Ca2+ dyshomeostasis impairs lysosomal acidification, lysosomal proteolytic activity and hinders autophagic-mediated protein aggregate clearance, which are processes vital to neuronal survival. These deficits were reversed by restoring intracellular Ca2+ homeostasis. Notably, this provides a therapeutic target and emphasizes the pathogenic relationship between ER-Ca2+ handling, that is known to be altered in AD, to pathogenic protein accumulation as a critical turning point in early stages of Alzheimers disease.

neuroscience↗

bioRxiv2021

Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria

Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central to defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multi-locus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which still harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors.

microbiology↗